Initial changes

ebi-gene-expression-group · Feb 11, 2024 · e286aba · e286aba
1 parent 85a3118
commit e286aba
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Showing 4 changed files with 10 additions and 6 deletions.
diff --git a/tools/tertiary-analysis/scanpy/scanpy-integrate-combat.xml b/tools/tertiary-analysis/scanpy/scanpy-integrate-combat.xml
@@ -8,7 +8,7 @@
   <command detect_errors="exit_code"><![CDATA[
 #if $batch_key
   ln -s '${input_obj_file}' input.h5 &&
-  PYTHONIOENCODING=utf-8 scanpy-integrate combat 
+  PYTHONIOENCODING=utf-8 scanpy-cli integrate combat 
   --batch-key '${batch_key}'
   #if $batch_layer
     --batch-layer '${batch_layer}'

diff --git a/tools/tertiary-analysis/scanpy/scanpy-integrate-harmony.xml b/tools/tertiary-analysis/scanpy/scanpy-integrate-harmony.xml
@@ -8,7 +8,7 @@
   <command detect_errors="exit_code"><![CDATA[
 #if $batch_key
   ln -s '${input_obj_file}' input.h5 &&
-  PYTHONIOENCODING=utf-8 scanpy-integrate harmony
+  PYTHONIOENCODING=utf-8 scanpy-cli integrate harmony
   --batch-key '${batch_key}'
   #if $basis
     --basis '${basis}'

diff --git a/tools/tertiary-analysis/scanpy/scanpy-multiplet-scrublet.xml b/tools/tertiary-analysis/scanpy/scanpy-multiplet-scrublet.xml
@@ -7,7 +7,7 @@
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
-PYTHONIOENCODING=utf-8 scanpy-multiplet scrublet 
+PYTHONIOENCODING=utf-8 scanpy-cli multiplet scrublet 
 #if $threshold
     --threshold '${threshold}'
 #end if

diff --git a/tools/tertiary-analysis/scanpy/scanpy_macros2.xml b/tools/tertiary-analysis/scanpy/scanpy_macros2.xml
@@ -1,7 +1,7 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.8.1</token>
+  <token name="@TOOL_VERSION@">1.9.3</token>
   <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
-  <token name="@PROFILE@">18.01</token>
+  <token name="@PROFILE@">20.09</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations,
@@ -69,8 +69,12 @@ EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.1.6">scanpy-scripts</requirement>
+      <!--
+        <requirement type="package" version="1.1.6">scanpy-scripts</requirement>
       <yield/>
+      This is provisional for testing and should be switched back to the package.
+      -->
+      <container type="docker">quay.io/biocontainers/scanpy-scripts:1.9.0--pyhdfd78af_0</container>
     </requirements>
   </xml>